Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample SCMH1 22955 broad.mit.edu 37 1 41503177 41503177 + Missense_Mutation SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr1:41503177G>A ENST00000402904.2 - 13 1873 c.1505C>T c.(1504-1506)tCc>tTc p.S502F SCMH1_ENST00000372596.1_Missense_Mutation_p.S441F|SCMH1_ENST00000361705.3_Missense_Mutation_p.S455F|SCMH1_ENST00000397174.2_Missense_Mutation_p.S482F|SCMH1_ENST00000372597.1_Missense_Mutation_p.S455F|SCMH1_ENST00000326197.7_Missense_Mutation_p.S502F|SCMH1_ENST00000456518.2_Missense_Mutation_p.S344F|SCMH1_ENST00000361191.5_Missense_Mutation_p.S441F|SCMH1_ENST00000397171.2_Missense_Mutation_p.S441F|SCMH1_ENST00000337495.5_Missense_Mutation_p.S512F|SCMH1_ENST00000372595.1_Missense_Mutation_p.S441F NM_001031694.2 NP_001026864.1 Q96GD3 SCMH1_HUMAN sex comb on midleg homolog 1 (Drosophila) 502 anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent DNA binding|sequence-specific DNA binding transcription factor activity breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1) 15 Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162) Myeloproliferative disorder(586;0.0393) TGGTTCCAAGGAGCGGGCCAG 0.532 24 80 --- --- --- --- S100A8 6279 broad.mit.edu 37 1 153362588 153362588 + Missense_Mutation SNP G G T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr1:153362588G>T ENST00000368733.3 - 3 442 c.273C>A c.(271-273)caC>caA p.H91Q S100A8_ENST00000368732.1_Missense_Mutation_p.H91Q NM_002964.4 NP_002955.2 P05109 S10A8_HUMAN S100 calcium binding protein A8 91 VAAHKKSHEESHKE -> WQPTKKAMKKATKSS (in Ref. 1; CAA68390). chemotaxis cytoplasm|cytoskeleton|plasma membrane calcium ion binding|protein binding breast(1)|endometrium(1)|lung(1)|urinary_tract(1) 4 all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.171) GCTACTCTTTGTGGCTTTCTT 0.468 18 88 --- --- --- --- RANBP2 5903 broad.mit.edu 37 2 109365442 109365442 + Missense_Mutation SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr2:109365442C>T ENST00000283195.6 + 9 1256 c.1130C>T c.(1129-1131)gCc>gTc p.A377V NM_006267.4 NP_006258.3 P49792 RBP2_HUMAN RAN binding protein 2 377 carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding RANBP2/ALK(34) NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1) 129 GAAACTTTTGCCAACAAAAGC 0.348 5 301 --- --- --- --- CNTNAP5 129684 broad.mit.edu 37 2 125547510 125547510 + Silent SNP A A G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr2:125547510A>G ENST00000431078.1 + 18 3145 c.2781A>G c.(2779-2781)ctA>ctG p.L927L NM_130773.2 NP_570129.1 Q8WYK1 CNTP5_HUMAN contactin associated protein-like 5 927 Laminin G-like 3. cell adhesion|signal transduction integral to membrane receptor binding NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3) 176 BRCA - Breast invasive adenocarcinoma(221;0.248) AAGGCTTCCTAGGATGCATTC 0.463 11 34 --- --- --- --- UGGT1 56886 broad.mit.edu 37 2 128917179 128917179 + Missense_Mutation SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr2:128917179C>T ENST00000375990.3 + 23 2778 c.2375C>T c.(2374-2376)gCa>gTa p.A792V UGGT1_ENST00000259253.6_Missense_Mutation_p.A816V Q9NYU2 UGGG1_HUMAN UDP-glucose glycoprotein glucosyltransferase 1 816 'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine endoplasmic reticulum lumen|ER-Golgi intermediate compartment UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 63 GCAATCTGGGCAGCTCTCCAA 0.478 16 63 --- --- --- --- IGSF11 152404 broad.mit.edu 37 3 118621499 118621499 + Silent SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr3:118621499G>A ENST00000354673.2 - 9 1541 c.1161C>T c.(1159-1161)agC>agT p.S387S IGSF11_ENST00000491903.1_Silent_p.S360S|IGSF11_ENST00000489689.1_Silent_p.S364S|IGSF11_ENST00000393775.2_Silent_p.S388S|IGSF11_ENST00000425327.2_Silent_p.S387S|IGSF11_ENST00000441144.2_Silent_p.S363S NM_152538.2 NP_689751.2 Q5DX21 IGS11_HUMAN immunoglobulin superfamily, member 11 388 cell adhesion|regulation of growth integral to membrane|plasma membrane receptor activity autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 34 CTGAGCCATTGCTCCTGGACA 0.527 14 40 --- --- --- --- WFS1 7466 broad.mit.edu 37 4 6302392 6302392 + Silent SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr4:6302392G>A ENST00000226760.1 + 8 1040 c.870G>A c.(868-870)aaG>aaA p.K290K WFS1_ENST00000503569.1_Silent_p.K290K NM_001145853.1|NM_006005.3 NP_001139325.1|NP_005996.2 O76024 WFS1_HUMAN Wolfram syndrome 1 (wolframin) 290 endoplasmic reticulum calcium ion homeostasis|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|glucose homeostasis|kidney development|negative regulation of neuron apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|polyubiquitinated misfolded protein transport|positive regulation of calcium ion transport|positive regulation of growth|positive regulation of protein ubiquitination|positive regulation of proteolysis|protein stabilization|renal water homeostasis|sensory perception of sound|visual perception dendrite|integral to endoplasmic reticulum membrane activating transcription factor binding|ATPase binding|transporter activity|ubiquitin protein ligase binding central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1) 21 Colorectal(103;0.0512) AGGTGGTCAAGTACCCCCTGC 0.617 11 19 --- --- --- --- RHOBTB3 22836 broad.mit.edu 37 5 95067675 95067675 + Nonsense_Mutation SNP G G T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr5:95067675G>T ENST00000379982.3 + 2 623 c.115G>T c.(115-117)Gag>Tag p.E39* RHOBTB3_ENST00000515852.1_3'UTR|CTD-2154I11.2_ENST00000513235.1_RNA|CTD-2154I11.2_ENST00000512486.1_RNA|RHOBTB3_ENST00000506817.1_Nonsense_Mutation_p.E39* NM_014899.3 NP_055714.3 O94955 RHBT3_HUMAN Rho-related BTB domain containing 3 39 Rho-like. retrograde transport, endosome to Golgi Golgi apparatus ATP binding|ATPase activity|Rab GTPase binding breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1) 16 all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198) all cancers(79;8.79e-16) CTCCGGGGACGAGAGCAGCTT 0.642 3 36 --- --- --- --- BAI3 577 broad.mit.edu 37 6 70071345 70071345 + Missense_Mutation SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr6:70071345G>A ENST00000370598.1 + 29 5001 c.4180G>A c.(4180-4182)Gat>Aat p.D1394N BAI3_ENST00000238918.8_Missense_Mutation_p.D600N|BAI3_ENST00000546190.1_Missense_Mutation_p.D358N NM_001704.2 NP_001695 O60242 BAI3_HUMAN brain-specific angiogenesis inhibitor 3 1394 negative regulation of angiogenesis|neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4) 210 all_lung(197;0.212) TGAGTTGGATGATAATGCAGG 0.403 27 49 --- --- --- --- SYNE1 23345 broad.mit.edu 37 6 152453342 152453342 + Missense_Mutation SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr6:152453342G>A ENST00000367255.5 - 144 26610 c.26009C>T c.(26008-26010)tCt>tTt p.S8670F SYNE1_ENST00000341594.5_Missense_Mutation_p.S8282F|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000354674.4_Missense_Mutation_p.S848F|SYNE1_ENST00000265368.4_Missense_Mutation_p.S8670F|SYNE1_ENST00000423061.1_Missense_Mutation_p.S8622F|SYNE1_ENST00000539504.1_Missense_Mutation_p.S825F|SYNE1_ENST00000356820.4_Missense_Mutation_p.S3194F|SYNE1_ENST00000448038.1_Missense_Mutation_p.S8622F NM_182961.3 NP_892006.3 Q8NF91 SYNE1_HUMAN spectrin repeat containing, nuclear envelope 1 8670 Ser-rich. cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex actin binding|lamin binding NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19) 524 Ovarian(120;0.0955) BRCA - Breast invasive adenocarcinoma(37;0.243) OV - Ovarian serous cystadenocarcinoma(155;2.24e-10) AGACCAGGAAGACAAATCCTA 0.512 HNSCC(10;0.0054) 24 86 --- --- --- --- CA13 377677 broad.mit.edu 37 8 86163132 86163132 + Silent SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr8:86163132C>T ENST00000321764.3 + 2 503 c.201C>T c.(199-201)ttC>ttT p.F67F CA13_ENST00000517298.1_3'UTR NM_198584.2 NP_940986.1 Q8N1Q1 CAH13_HUMAN carbonic anhydrase XIII 67 one-carbon metabolic process carbonate dehydratase activity|zinc ion binding p.F67F(2) large_intestine(1)|lung(6) 7 GCCATTCCTTCAATGTTGACT 0.398 5 221 --- --- --- --- PSAT1 29968 broad.mit.edu 37 9 80923474 80923474 + Silent SNP T T C TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr9:80923474T>C ENST00000376588.3 + 6 783 c.715T>C c.(715-717)Ttg>Ctg p.L239L PSAT1_ENST00000347159.2_Silent_p.L239L NM_058179.2 NP_478059.1 Q9Y617 SERC_HUMAN phosphoserine aminotransferase 1 239 L-serine biosynthetic process|pyridoxine biosynthetic process O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1) 20 L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165) AAACAGCTCCTTGTACAACAC 0.537 3 59 --- --- --- --- SETX 23064 broad.mit.edu 37 9 135153581 135153581 + Missense_Mutation SNP T T G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr9:135153581T>G ENST00000372169.2 - 21 6900 c.6718A>C c.(6718-6720)Aat>Cat p.N2240H SETX_ENST00000224140.5_Missense_Mutation_p.N2240H|SETX_ENST00000393220.1_Missense_Mutation_p.N2240H Q7Z333 SETX_HUMAN senataxin 2240 cell death|double-strand break repair|RNA processing cytoplasm|nucleolus|nucleoplasm ATP binding|DNA helicase activity breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2) 97 Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171) TGTTCTACATTCTCTTCCAGC 0.453 16 77 --- --- --- --- DLG5 9231 broad.mit.edu 37 10 79571813 79571813 + Silent SNP G G A TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr10:79571813G>A ENST00000372391.2 - 22 4196 c.4191C>T c.(4189-4191)ttC>ttT p.F1397F DLG5_ENST00000372388.2_Silent_p.F1057F|DLG5_ENST00000459739.1_5'UTR NM_004747.3 NP_004738.3 Q8TDM6 DLG5_HUMAN discs, large homolog 5 (Drosophila) 1397 PDZ 3. cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis cell junction|cytoplasm beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 60 all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146) Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446) TTATGCCGTTGAACTGGGGAA 0.647 10 43 --- --- --- --- LRIT1 26103 broad.mit.edu 37 10 85992631 85992631 + Silent SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr10:85992631C>T ENST00000372105.3 - 4 945 c.924G>A c.(922-924)acG>acA p.T308T NM_015613.2 NP_056428.1 Q9P2V4 LRIT1_HUMAN leucine-rich repeat, immunoglobulin-like and transmembrane domains 1 308 Ig-like C2-type. integral to endoplasmic reticulum membrane breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1) 23 GAGTCCAGCTCGTGCCGTCAC 0.572 8 30 --- --- --- --- MORN4 118812 broad.mit.edu 37 10 99376049 99376049 + Missense_Mutation SNP A A T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr10:99376049A>T ENST00000335628.3 - 4 585 c.586T>A c.(586-588)Tcc>Acc p.S196T PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron|MORN4_ENST00000478953.1_3'UTR|MORN4_ENST00000307450.6_Missense_Mutation_p.S138T Q8NDC4 MORN4_HUMAN MORN repeat containing 4 138 large_intestine(1)|lung(1)|stomach(2) 4 GCTGACTTGGAGGCGCTCTGG 0.532 3 32 --- --- --- --- SIDT2 51092 broad.mit.edu 37 11 117052521 117052521 + Splice_Site SNP A A G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr11:117052521A>G ENST00000324225.4 + 3 836 c.e3-1 SIDT2_ENST00000431081.2_Splice_Site|SIDT2_ENST00000530948.1_Splice_Site NM_001040455.1 NP_001035545.1 Q8NBJ9 SIDT2_HUMAN SID1 transmembrane family, member 2 integral to membrane|lysosomal membrane NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2) 36 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144) TTCGGGCCATAGGTTTCAGCG 0.592 OREG0021368 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 3 55 --- --- --- --- ATN1 1822 broad.mit.edu 37 12 7048124 7048124 + Missense_Mutation SNP C C G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr12:7048124C>G ENST00000356654.4 + 7 3235 c.2998C>G c.(2998-3000)Cga>Gga p.R1000G ATN1_ENST00000396684.2_Missense_Mutation_p.R1000G NM_001007026.1 NP_001007027.1 P54259 ATN1_HUMAN atrophin 1 1000 cell death|central nervous system development cytoplasm|nucleus protein domain specific binding breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2) 40 GCCCCTGGAGCGAGAACGTCT 0.682 22 84 --- --- --- --- CCER1 196477 broad.mit.edu 37 12 91347894 91347894 + Missense_Mutation SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr12:91347894C>T ENST00000358859.2 - 1 1059 c.626G>A c.(625-627)cGt>cAt p.R209H CCER1_ENST00000548187.1_Intron NM_152638.2 NP_689851.1 coiled-coil glutamate-rich protein 1 CTCCTGCTGACGCTCCACCTT 0.647 12 95 --- --- --- --- MAP1A 4130 broad.mit.edu 37 15 43817506 43817506 + Missense_Mutation SNP A A G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr15:43817506A>G ENST00000382031.1 + 5 4580 c.4549A>G c.(4549-4551)Atc>Gtc p.I1517V MAP1A_ENST00000399453.1_Missense_Mutation_p.I1279V|MAP1A_ENST00000300231.5_Missense_Mutation_p.I1279V P78559 MAP1A_HUMAN microtubule-associated protein 1A 1279 cytoplasm|microtubule|microtubule associated complex protein binding|structural molecule activity breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 66 all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;3.05e-06) Estramustine(DB01196) ACAGACAGACATCACAGATGA 0.542 4 39 --- --- --- --- USP31 57478 broad.mit.edu 37 16 23116855 23116855 + Missense_Mutation SNP G G C TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr16:23116855G>C ENST00000219689.7 - 5 995 c.996C>G c.(994-996)caC>caG p.H332Q NM_020718.3 NP_065769.3 Q70CQ4 UBP31_HUMAN ubiquitin specific peptidase 31 332 ubiquitin-dependent protein catabolic process cysteine-type peptidase activity|ubiquitin thiolesterase activity breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2) 57 GBM - Glioblastoma multiforme(48;0.0187) TCCTCATGCAGTGAGAACATT 0.433 6 60 --- --- --- --- ZNF420 147923 broad.mit.edu 37 19 37619569 37619569 + Missense_Mutation SNP A A G TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr19:37619569A>G ENST00000337995.3 + 5 1891 c.1676A>G c.(1675-1677)tAt>tGt p.Y559C ZNF420_ENST00000586540.1_3'UTR|ZNF420_ENST00000304239.7_Intron|ZNF585A_ENST00000588723.1_Intron NM_144689.3 NP_653290.2 Q8TAQ5 ZN420_HUMAN zinc finger protein 420 559 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3) 27 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) GAGAAACCATATCAATGTAAG 0.418 4 59 --- --- --- --- MIR519A2 574500 broad.mit.edu 37 19 54265626 54265626 + RNA SNP C C T rs142071806 by1000genomes TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr19:54265626C>T ENST00000384990.1 + 0 29 NR_030222.1 TACAGGGAAGCGCTTTCTGTT 0.408 27 115 --- --- --- --- LILRB3 11025 broad.mit.edu 37 19 54721088 54721088 + Silent SNP G G T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr19:54721088G>T ENST00000391750.1 - 14 1906 c.1770C>A c.(1768-1770)tcC>tcA p.S590S LILRB3_ENST00000245620.9_Silent_p.S591S|LILRA6_ENST00000419410.2_Silent_p.S591S|LILRB3_ENST00000424807.1_Silent_p.S590S|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Silent_p.S607S|LILRA6_ENST00000440558.2_Silent_p.S590S|LILRA6_ENST00000270464.5_Silent_p.S591S|LILRB3_ENST00000346401.6_Silent_p.S602S O75022 LIRB3_HUMAN leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 590 cell surface receptor linked signaling pathway|defense response integral to plasma membrane transmembrane receptor activity endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1) 34 all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19) GBM - Glioblastoma multiforme(193;0.105) TCACATCCTGGGAGGCTTCAG 0.637 14 45 --- --- --- --- PTPRH 5794 broad.mit.edu 37 19 55693512 55693512 + Missense_Mutation SNP C C T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr19:55693512C>T ENST00000376350.3 - 19 3092 c.3070G>A c.(3070-3072)Gtg>Atg p.V1024M PTPRH_ENST00000263434.5_Missense_Mutation_p.V846M NM_002842.3 NP_002833.3 Q9HD43 PTPRH_HUMAN protein tyrosine phosphatase, receptor type, H 1024 Tyrosine-protein phosphatase. apoptosis cytoplasm|integral to plasma membrane protein binding|transmembrane receptor protein tyrosine phosphatase activity breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2) 67 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0479) GTGCGACCCACGCCAGCACTA 0.587 17 64 --- --- --- --- ZNF471 57573 broad.mit.edu 37 19 57036932 57036932 + Missense_Mutation SNP G G T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr19:57036932G>T ENST00000308031.5 + 5 1629 c.1496G>T c.(1495-1497)aGt>aTt p.S499I ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron NM_020813.2 NP_065864.2 Q9BX82 ZN471_HUMAN zinc finger protein 471 499 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 36 Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) GBM - Glioblastoma multiforme(193;0.0307) TTTAGAATCAGTTCACAGCTG 0.378 17 45 --- --- --- --- SSX3 10214 broad.mit.edu 37 X 48207020 48207020 + Missense_Mutation SNP A A T TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chrX:48207020A>T ENST00000298396.2 - 7 538 c.486T>A c.(484-486)caT>caA p.H162Q SSX3_ENST00000376895.1_Missense_Mutation_p.H74Q NM_021014.2 NP_066294.1 Q99909 SSX3_HUMAN synovial sarcoma, X breakpoint 3 162 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding endometrium(3)|large_intestine(1)|lung(9) 13 GGGTCCAGGCATGTTCCCCCC 0.478 66 112 --- --- --- --- RANBP2 5903 broad.mit.edu 37 2 109382805 109382805 + Frame_Shift_Del DEL T T - TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr2:109382805delT ENST00000283195.6 + 20 5936 c.5810delT c.(5809-5811)attfs p.I1937fs NM_006267.4 NP_006258.3 P49792 RBP2_HUMAN RAN binding protein 2 1937 carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding RANBP2/ALK(34) NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1) 129 CGTGGTGTGATTTTTGGCCAA 0.413 7 539 --- --- --- --- PROC 5624 broad.mit.edu 37 2 128186333 128186333 + Frame_Shift_Del DEL G G - TCGA-YL-A8SK-01B-21D-A377-08 TCGA-YL-A8SK-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 90b319c1-a436-4ade-bade-62393163aeaf 8a62da06-7d92-47d9-86fe-07676e6ac836 g.chr2:128186333delG ENST00000453608.2 + 8 1370 c.1362delG c.(1360-1362)gagfs p.E454fs PROC_ENST00000422777.3_Frame_Shift_Del_p.E399fs|PROC_ENST00000234071.3_Frame_Shift_Del_p.E399fs|PROC_ENST00000409048.1_Frame_Shift_Del_p.E433fs P04070 PROC_HUMAN protein C (inactivator of coagulation factors Va and VIIIa) 399 blood coagulation|leukocyte migration|negative regulation of apoptosis|negative regulation of blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis endoplasmic reticulum lumen|Golgi lumen|plasma membrane calcium ion binding|protein binding|serine-type endopeptidase activity endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1) 15 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0673) Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464) ATGCCTGCGAGGGCGACAGTG 0.652 18 99 --- --- --- ---